Unfortunately, this doesn't just affect the root filesystem. For example, I recently installed Ubuntu Netbook Remix 9.04 on an Eeepc 901, with /home residing on a 16 GB SD card... rootfs is on internal storage. I soon discovered that when running on battery power, however, the SD card usually isn't available when the filesystems get mounted.
My current workaround is to check if /home is present in /etc/rc.local, and re-attempt the mount if necessary. I'm definitely on the lookout for a better fix, but at the time needed to get it working rather quickly.